[BioC] time course analyses Illumina RNA-seq data

Ryan C. Thompson rct at thompsonclan.org
Wed Mar 13 20:04:10 CET 2013

As far as I'm aware, the same strategy described for doing limma time 
course analysis with splines would  also apply to GLM-based methods for 
RNA-seq like edgeR,

On Wed 13 Mar 2013 10:55:13 AM PDT, Steve Lianoglou wrote:
> Hi Sandra,
> On Wed, Mar 13, 2013 at 12:22 PM, Sandra Rehan <sandra.rehan at gmail.com> wrote:
>> I am looking for software to analyze time course data for an Illumina
>> gene expression data set (four lanes of paired end reads). I have two
>> biological replicates for seven time points. All packages that I am
>> aware of (bats, time course, edge) are designed for microarray data
>> analysis. Does someone know of a software package designed for
>> Illumina time course data?
> There has been a recent thread on this list about doing a "proper"
> timecourse analysis w/ limma using splines -- this thread resulted in
> Gordon adding an additional section to the limma user's guide on how
> to do so.
> I wonder if you couldn't just use limma::voom to hammer your data into
> a limma-workable-object and just do the timecourse analysis as
> suggested w/ the microarray data?
> HTH,
> -steve

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